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authorJohannes Ranke <jranke@uni-bremen.de>2021-02-03 16:41:31 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2021-02-03 18:18:19 +0100
commitf0ef23a7598e5d19648ae4edc2b74e0fba27a41c (patch)
tree03af20e730330e148acf3a7c008d82387dbe52eb /R/plot.mixed.mmkin.R
parent82814b17ec182467c25325d747fffa8ffbe4bb33 (diff)
Prepare for v1.0.0v1.0.0
- Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest
Diffstat (limited to 'R/plot.mixed.mmkin.R')
-rw-r--r--R/plot.mixed.mmkin.R23
1 files changed, 1 insertions, 22 deletions
diff --git a/R/plot.mixed.mmkin.R b/R/plot.mixed.mmkin.R
index 1674d855..5a0b7412 100644
--- a/R/plot.mixed.mmkin.R
+++ b/R/plot.mixed.mmkin.R
@@ -2,7 +2,7 @@ utils::globalVariables("ds")
#' Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object
#'
-#' @param x An object of class [mixed.mmkin], [saem.mmkin] or [nlme.mmkin]
+#' @param x An object of class [mixed.mmkin], [nlme.mmkin]
#' @param i A numeric index to select datasets for which to plot the individual predictions,
#' in case plots get too large
#' @inheritParams plot.mkinfit
@@ -39,15 +39,6 @@ utils::globalVariables("ds")
#' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3))
#' plot(f_nlme)
#'
-#' f_saem <- saem(f, transformations = "saemix")
-#' plot(f_saem)
-#'
-#' # We can overlay the two variants if we generate predictions
-#' pred_nlme <- mkinpredict(dfop_sfo,
-#' f_nlme$bparms.optim[-1],
-#' c(parent = f_nlme$bparms.optim[[1]], A1 = 0),
-#' seq(0, 180, by = 0.2))
-#' plot(f_saem, pred_over = list(nlme = pred_nlme))
#' }
#' @export
plot.mixed.mmkin <- function(x,
@@ -91,18 +82,6 @@ plot.mixed.mmkin <- function(x,
type = ifelse(standardized, "pearson", "response"))
}
- if (inherits(x, "saem.mmkin")) {
- if (x$transformations == "saemix") backtransform = FALSE
- degparms_i <- saemix::psi(x$so)
- rownames(degparms_i) <- ds_names
- degparms_i_names <- setdiff(x$so@results@name.fixed, names(fit_1$errparms))
- colnames(degparms_i) <- degparms_i_names
- residual_type = ifelse(standardized, "standardized", "residual")
- residuals <- x$data[[residual_type]]
- degparms_pop <- x$so@results@fixed.effects
- names(degparms_pop) <- degparms_i_names
- }
-
degparms_fixed <- fit_1$fixed$value
names(degparms_fixed) <- rownames(fit_1$fixed)
degparms_all <- cbind(as.matrix(degparms_i),

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